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. 2015 Sep 24:6:298.
doi: 10.3389/fgene.2015.00298. eCollection 2015.

Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout

Sixin Liu  1 , Roger L Vallejo  1 , Yniv Palti  1 , Guangtu Gao  1 , David P Marancik  1 , Alvaro G Hernandez  2 , Gregory D Wiens  1
Affiliations

Identification of single nucleotide polymorphism markers associated with bacterial cold water disease resistance and spleen size in rainbow trout

Sixin Liu et al. Front Genet. .

Abstract

Bacterial cold water disease (BCWD) is one of the frequent causes of elevated mortality in salmonid aquaculture. Previously, we identified and validated microsatellites on chromosome Omy19 associated with QTL (quantitative trait loci) for BCWD resistance and spleen size in rainbow trout. Recently, SNPs (single nucleotide polymorphism) have become the markers of choice for genetic analyses in rainbow trout as they are highly abundant, cost-effective and are amenable for high throughput genotyping. The objective of this study was to identify SNP markers associated with BCWD resistance and spleen size using both genome-wide association studies (GWAS) and linkage-based QTL mapping approaches. A total of 298 offspring from the two half-sib families used in our previous study to validate the significant BCWD QTL on chromosome Omy19 were genotyped with RAD-seq (restriction-site-associated DNA sequencing), and 7,849 informative SNPs were identified. Based on GWAS, 18 SNPs associated with BCWD resistance and 20 SNPs associated with spleen size were identified. Linkage-based QTL mapping revealed three significant QTL for BCWD resistance. In addition to the previously validated dam-derived QTL on chromosome Omy19, two significant BCWD QTL derived from the sires were identified on chromosomes Omy8 and Omy25, respectively. A sire-derived significant QTL for spleen size on chromosome Omy2 was detected. The SNP markers reported in this study will facilitate fine mapping to identify positional candidate genes for BCWD resistance in rainbow trout.

Keywords: Flavobacterium psychrophilum; QTL; SNP; bacterial cold water disease; rainbow trout; spleen size.

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Figures

FIGURE 1
FIGURE 1
Results of genome-wide association studies of survival status using GenABEL’s GRAMMAR-Gamma method. The horizontal lines represent P = 1 × 10-3 and P = 1 × 10-5, respectively.
FIGURE 2
FIGURE 2
Results of genome-wide association studies of survival days using GenABEL’s GRAMMAR-Gamma method. The horizontal lines represent P = 1 × 10-3 and P = 1 × 10-5, respectively.
FIGURE 3
FIGURE 3
Results of genome-wide association studies of spleen index using GenABEL’s GRAMMAR-Gamma method. The horizontal lines represent P = 1 × 10-3 and P = 1 × 10-5, respectively.
See this image and copyright information in PMC

References

    1. Aulchenko Y. S., Ripke S., Isaacs A., Van Duijn C. M. (2007). GenABEL: an R library for genorne-wide association analysis. Bioinformatics 23 1294–1296. 10.1093/bioinformatics/btm108 - DOI - PubMed
    1. Baird N. A., Etter P. D., Atwood T. S., Currey M. C., Shiver A. L., Lewis Z. A., et al. (2008). Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS ONE 3:e3376 10.1371/journal.pone.0003376 - DOI - PMC - PubMed
    1. Berthelot C., Brunet F., Chalopin D., Juanchich A., Bernard M., Noel B., et al. (2014). The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat. Commun. 5 3657 10.1038/ncomms4657 - DOI - PMC - PubMed
    1. Campbell N. R., Lapatra S. E., Overturf K., Towner R., Narum S. R. (2014). Association mapping of disease resistance traits in rainbow trout using restriction site associated DNA sequencing. G3 (Bethesda) 4 2473–2481. 10.1534/g3.114.014621 - DOI - PMC - PubMed
    1. Hadidi S., Glenney G. W., Welch T. J., Silverstein J. T., Wiens G. D. (2008). Spleen size predicts resistance of rainbow trout to Flavobacterium psychrophilum challenge. J. Immunol. 180 4156–4165. 10.4049/jimmunol.180.6.4156 - DOI - PubMed

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